Gene and protein expression profiles associated with the therapeutic efficacy of EGFR-TK inhibitors

ABSTRACT

The present invention provides protein and gene expression profiles indicative of whether a patient afflicted with non-small cell lung cancer is likely to be responsive to treatment with a therapeutic compound that is a EGFR-TK inhibitor. By identifying such responsiveness, a treatment provider may determine in advance those patients who would benefit from such treatment, as well as identify alternative therapies for non-responders. The present invention further provide methods of using the gene and protein expression profiles, and assays for identifying the presence of a gene or protein expression profile in a patient sample.

RELATED APPLICATIONS

This application is a Divisional patent application of Ser. No. 12/072,651 filed 27 Feb. 2008 which claims priority under 35 U.S.C. §119(e) to U.S. Provisional Application Ser. No. 60/903,684 filed Feb. 27, 2007, the entirety of which is incorporated herein by reference.

BACKGROUND OF THE INVENTION

Patients diagnosed with cancer are faced with costly and often painful treatment options. These treatments may be ineffective in a subpopulation of patients, and as a result, these patients endure these treatments without little or no therapeutic benefit. Some patients may react adversely to certain agents causing additional suffering and possibly death.

Ineffective treatment also is problematic because time is a key variable when treating cancer. A treatment provider has a far greater chance of containing and managing the disease if the cancer is diagnosed at an early stage and treated with a therapeutically effective agent. An agent may provide great therapeutic benefits if administered at an early stage of the disease; however, with the passage of time, the same agent may cease to be effective.

Lung cancer is an example of a condition where early diagnosis is key for effective treatment. Most lung cancers fall into one of two categories: small cell lung cancer and non-small cell lung cancer (NSCLC). NSCLC is the most common type of lung cancer. There are three main subgroups of NSCLC: adenocarcinoma, squamous cell carcinoma and large cell undifferentiated carcinoma.

Chemotherapy often is used for treating NSCLC. Erlotinib (TARCEVA®) is a chemotherapeutic agent indicated for second-line therapy of NSCLC after failure of at least one prior chemotherapy regimen and gefitinib (IRESSA®) is indicated for continued treatment of NSCLC after failure of platinum-based and docetaxel chemotherapies. As with many chemotherapeutic agents, administration of these drugs often causes deleterious side effects for the patient, and some patients do not respond well, or respond at all, to the treatment. Some patients thus undergo treatment with erlotinib or gefitinib and suffer the painful side effects only to later realize that the agent has not been therapeutically beneficial to their condition. In addition to the unnecessary suffering, critical time is lost in determining an alternative treatment.

SUMMARY OF THE INVENTION

The present invention provides gene and protein expression profiles and methods for using them to identify those patients who are likely to respond to treatment with compounds that inhibit the intracellular phosphorylation of tyrosine kinase (TK) associated with epidermal growth factor receptor (EGFR), including erlotinib and gefitinib (these patients are referred to as “responders”), as well as those patients who are not likely to benefit from such treatment (these patients are referred to as “non-responders”). The present invention allows a treatment provider to identify those patients who are responders to treatment with compounds that inhibit the intracellular phosphorylation of EGFR-associated tyrosine kinase, including erlotinib and gefitinib, and those who are non-responders to such treatment, prior to administration of the agent. Compounds such as erlotinib and gefitinib that inhibit the intracellular phosphorylation of EGFR-associated tyrosine kinase are referred to hereinafter as EGFR-TK inhibitors.

The present invention comprises protein expression profiles, as well as the corresponding gene expression profiles (also referred to as “gene signatures”) that are indicative of the tendency of a patient afflicted with lung cancer, particularly NSCLC, to respond to treatment with an EGFR-TK inhibitor. The protein expression profile comprises at least one, and preferably a plurality, of proteins selected from the group consisting of p70S6K, phospho-p70S6, phospho-S6, phospho-AKT, phospho-mTOR, phospho-pTEN, phospho MEK, phospho MAPK, phospho-IGFR/InR, EGFR, phospho-EGFR, phospho-HER2/ErbB2, phospho-ER, phospho-AR, AIK, osteopontin, MMP11 and GFAP. This group of proteins is referred to herein as the “EGFR-TK Inhibitor Responder Proteins”. According to the invention, some or all of these proteins are differentially expressed (e.g., up-regulated or down-regulated) in patients who are responders to EGFR-TK inhibitor therapy. Specifically, p70S6K, phospho-S6, phospho-AKT, phospho-mTOR, phospho-pTEN, EGFR, phospho-ER, phospho-AR, AIK, osteopontin, MMP11 and GFAP are up-regulated (over-expressed) and phospho-p70S6, phospho MEK, phospho MAPK, phospho-IGFR/InR, phospho-EGFR and phospho-HER2/ErbB2 are down-regulated (under expressed) in patients who are responders to EGFR-TK inhibitors.

The present invention further comprises gene expression profiles (also referred to as “gene signatures”) that are indicative of the tendency of a patient afflicted with NSCLC to respond to treatment with an EGFR-TK inhibitor. The gene expression profile comprises at least one, and preferably a plurality, of genes that encode the proteins selected from the group consisting of p70S6K, phospho-p70S6, phospho-S6, phospho-AKT, phospho-mTOR, phospho-pTEN, phospho MEK, phospho MAPK, phospho-IGFR/InR, EGFR, phospho-EGFR, phospho-HER2/ErbB2, phospho-ER, phospho-AR, AIK, osteopontin, MMP11 and GFAP. This group of genes is referred to herein as the “EGFR-TK Inhibitor Responder Genes”. According to the invention, some or all of theses genes are differentially expressed (e.g., up-regulated or down-regulated) in patients who are responders to EGFR-TK inhibitor therapy. Specifically, the genes encoding p70S6K, phospho-S6, phospho-AKT, phospho-mTOR, phospho-pTEN, EGFR, phospho-ER, phospho-AR, AIK, osteopontin, MMP11 and GFAP are up-regulated (over-expressed) and the genes encoding phospho-p70S6, phospho MEK, phospho MAPK, phospho-IGFR/InR, phospho-EGFR and phospho-HER2/ErbB2 are down-regulated (under expressed) in patients who are responders to EGFR-TK inhibitors.

The present invention further comprises a method of determining if a patient is a responder or non-responder to treatment with an EGFR-TK inhibitor. The method comprises obtaining a tumor sample from the patient, determining the protein and/or gene expression profile of the sample, and determining from the gene expression profile whether at least one protein selected from the to EGFR-TK inhibitor Responder Proteins and/or the EGFR-TK Inhibitor Responder Genes is over- or under-expressed in the sample. From this information, the treatment provider can ascertain whether the patient is likely to benefit from to EGFR-TK inhibitor therapy.

The present invention further comprises an assay for determining the protein and/or gene expression profile in a patient's sample, and instructions for using the assay.

DETAILED DESCRIPTION

The present invention provides gene and protein expression profiles (GPEPs), and their use for predicting a patient's responsiveness to a cancer treatment. More specifically, the present gene and protein expression profiles are indicative of whether a patient afflicted with non small cell lung cancer (NSCLC) is a responder or a non-responder to treatment with a compound which is an EGFR-TK inhibitor, in particular, erlotinib (TARCEVA®) or gefitinib (IRESSA®).

Erlotinib and gefitinib are chemotherapeutic agents which belong to the group of medicines called antineoplastics. These compounds act by inhibiting the intracellular phoshorylation of tyrosine kinase associated with transmembrane cell surface receptors, including EGFR, a receptor expressed on the cell surface of normal cells and cancer cells. These compounds interfere with the growth of cancer cells, which are eventually destroyed.

Significant improvements in the outcomes of NSCLC in some patients treated with erlotinib or gefitinib have been reported. However, the growth of normal cells often is affected by these medicines, causing unwanted and/or unpleasant effects. These other effects may include: diarrhea, rash, acne, dry skin, nausea (feeling sick) and vomiting, loss of appetite and weight loss, asthenia and pruritis and abdominal pain. The present invention provides biomarkers that are associated with those patients that have benefited from treatment with erlotinib and/or gefitinib. The present invention thus enables the treatment provider to determine in advance those NSCLC patients likely to benefit from treatment with erlotinib or gefitinib, and to consider alternative treatment options for non-responders.

In one embodiment, the present invention provides protein expression profiles that are indicative of whether a patient is likely to be a responder or non-responder to EGFR-TK inhibitor therapy. The proteins comprising the expression profile disclosed herein are selected from the group consisting of p70S6K, phospho-p70S6, phospho-S6, phospho-AKT, phospho-mTOR, phospho-pTEN, phospho MEK, phospho MAPK, phospho-IGFR/InR, EGFR, phospho-EGFR, phospho-HER2/ErbB2, phospho-ER, phospho-AR, AIK, osteopontin, MMP11 and GFAP. This group of proteins is referred to herein as the “EGFR-TK Inhibitor Responder Proteins”. According to the invention, some or all of these proteins are differentially expressed (e.g., up-regulated or down-regulated) in patients who are responders to EGFR-TK inhibitor therapy. Specifically, p70S6K, phospho-S6, phospho-AKT, phospho-mTOR, phospho-pTEN, EGFR, phospho-ER, phospho-AR, AIK, osteopontin, MMP11 and GFAP are up-regulated (over-expressed) and phospho-p70S6, phospho MEK, phospho MAPK, phospho-IGFR/InR, phospho-EGFR and phospho-HER2/ErbB2 are down-regulated (under expressed) in patients who are responders to EGFR-TK inhibitors.

Table 1 identifies the EGFR-TK inhibitor Responder Proteins, and indicates whether expression of these proteins is up- or down-regulated in patients that are responders to therapy with an EGFR-TK inhibitor.

TABLE 1 Protein* Over Under SEQ ID No. of Accession No. Expression Expression Protein Total p70S6K Pos 17 NP_003152 Phospho-p70S6 Pos Same as above Phospho-S6 Pos 18 NP_001001 Phospho-AKT Pos 19 NP_005154 Phospho-mTOR Pos 20 NP_004949 Phospho-PTEN Pos 21 NP_000305 Phospho MEK Pos 22 NP_002746 Phospho MAPK Pos 23 NP_002736 Phospho-IGFR1/InR Pos 24 NP_000557 Total EGFR Pos 25 NP_005219 Phospho-EGFR Pos Same as above Phospho-HER2(ErbB2) Pos 26 NP_001005862 Phospho-ER Pos 27 NP_000116 Phospho-AR Pos 28 NP_000035 AIK Pos 29 NP_940835 Osteopontin Pos 30 NP_000573 MMP11 Pos 31 NP_005931 GFAP Pos 32 NP_002046 *Accession No. refers to non-phosphorylated protein

The present invention further comprises gene expression profiles that are indicative of the tendency of a patient afflicted with NSCLC to respond to treatment with EGFR-TK inhibitors. The gene expression profile comprises at least one, and preferably a plurality, of genes that encode the proteins selected from the group consisting of p70S6K, phospho-p70S6, phospho-S6, phospho-AKT, phospho-mTOR, phospho-pTEN, phospho MEK, phospho MAPK, phospho-IGFR/InR, EGFR, phospho-EGFR, phospho-HER2/ErbB2, phospho-ER, phospho-AR, AIK, osteopontin, MMP11 and GFAP. This group of proteins is referred to herein as the “EGFR-TK Inhibitor Responder Genes”. According to the invention, some or all of theses genes are differentially expressed (e.g., up-regulated or down-regulated) in patients who are responders to EGFR-TK inhibitor therapy. Specifically, the genes encoding p70S6K, phospho-S6, phospho-AKT, phospho-mTOR, phospho-pTEN, EGFR, phospho-ER, phospho-AR, AIK, osteopontin, MMP11 and GFAP are up-regulated (over-expressed) and the genes encoding phospho-p70S6, phospho MEK, phospho MAPK, phospho-IGFR/InR, phospho-EGFR and phospho-HER2/ErbB2 are down-regulated (under expressed) in patients who are responders to EGFR-TK inhibitors. Accordingly, it is possible to determine in advance if a patient is likely to benefit form such therapy by obtaining a gene expression profile from the patient's tissue, and determining whether one or more of the genes in the EGFR-TK inhibitor Responder Genes is up- or down-regulated.

Table 2 identifies the EGFR-TK Inhibitor Responder Genes and indicates whether expression of these genes is up- or down-regulated in patients that are responders to therapy with an EGFR-TK inhibitor. Table 2 also sets forth the NCBI Accession Number of at least one variant of these genes.

TABLE 2 Gene Over Under SEQ Accession Ex- Ex- ID. No. Number Encoded Protein pression pression of Genes RPS6KB1 Total p70S6K Pos 1 NM_003161 Same as above Phospho-p70S6 Pos RPS6 Phospho-S6 Pos 2 NM_001010 AKT1 Phospho-AKT Pos 3 NM_005163 FRAP1 Phospho-mTOR Pos 4 NM_004958 PTEN Phospho-PTEN Pos 5 NM_000314 MAP2K1 Phospho MEK Pos 6 NM_002755 MAPK1 Phospho MAPK Pos 7 NM_002745 FCGR1A Phospho- Pos 8 NM_000566 IGFR1/InR EGFR Total EGFR Pos 9 NM_005228 Same as above Phospho-EGFR Pos ERBB2 Phospho- Pos 10 NM_001005862 HER2(ErbB2) ESR1 Phospho-ER Pos 11 NM_000125 AR Phospho-AR Pos 12 NM_000044 AURKA AIK Pos 13 NM_198433 SPP1 Osteopontin Pos 14 NM_000582 MMP11 MMP11 Pos 15 NM_005940 GFAP GFAP Pos 16 NM_002055

Other variants of these genes exist (e.g., see the gene databases available through the NCBI Entrez website (www.ncbi.nlm.nih.gov/gquery), and these variants are encompassed by the present invention.

In a preferred aspect of the present invention, the protein expression profiles of the present invention comprise at least about four, preferably between about four and nine, and more preferably between about nine and eighteen of the EGFR-TK Inhibitor Responder Proteins that are up- or down-regulated as applicable. In a currently preferred embodiment, the protein expression profile comprises at least about four, and preferably about six to twelve, of the EGFR-TK Inhibitor Responder Proteins that are up-regulated, and at least about two, and preferably about four to six, of the EGFR-TK Inhibitor Responder Proteins that are down-regulated.

In a preferred aspect of the present invention, the gene expression profiles of the present invention comprise at least about four, preferably between about four and nine, and more preferably between about nine and sixteen of the EGFR-TK Inhibitor Responder Genes that are up- or down-regulated as applicable. In a currently preferred embodiment, the gene expression profile comprises at least about four, and preferably about six to twelve, of the EGFR-TK Inhibitor Responder Genes that are up-regulated, and at least about two, and preferably about four to six, of the EGFR-TK Inhibitor Responder Genes that are down-regulated.

The protein and/or gene expression profiles of the invention can be used to predict the responsiveness of a NSCLC patient to therapy with an EGFR-TK inhibitor, in particular, erlotinib or gefitinib. In one aspect, the present method comprises (a) obtaining a protein or gene expression profile from a tumor sample of a patient afflicted with NSCLC; (b) determining from the protein or gene expression profile whether expression of one or more of the following proteins is up-regulated (over-expressed): p70S6K, phospho-S6, phospho-AKT, phospho-mTOR, phospho-pTEN, EGFR, phospho-ER, phospho-AR, AIK, osteopontin, MMP11 and GFAP; and/or whether expression of at least one of the following proteins is down-regulated (under-expressed): phospho-p70S6, phospho MEK, phospho MAPK, phospho-IGFR/InR, phosho-EGFR and phospho-HER2(ErbB2). The predictive value of the protein or gene profile for determining response to these compounds increases with the number of these proteins or the associated genes that are found to be up- or down-regulated in accordance with the invention. Preferably, at least about four, more preferably between about four and nine, and most preferably between about nine and eighteen of the EGFR-TK Responder Proteins or Genes are differentially expressed.

DEFINITIONS

For convenience, the meaning of certain terms and phrases employed in the specification, examples, and appended claims are provided below. The definitions are not meant to be limiting in nature and serve to provide a clearer understanding of certain aspects of the present invention.

The term “genome” is intended to include the entire DNA complement of an organism, including the nuclear DNA component, chromosomal or extrachromosomal DNA, as well as the cytoplasmic domain (e.g., mitochondrial DNA).

The term “gene” refers to a nucleic acid sequence that comprises control and coding sequences necessary for producing a polypeptide or precursor. The polypeptide may be encoded by a full length coding sequence or by any portion of the coding sequence. The gene may be derived in whole or in part from any source known to the art, including a plant, a fungus, an animal, a bacterial genome or episome, eukaryotic, nuclear or plasmid DNA, cDNA, viral DNA, or chemically synthesized DNA. A gene may contain one or more modifications in either the coding or the untranslated regions that could affect the biological activity or the chemical structure of the expression product, the rate of expression, or the manner of expression control. Such modifications include, but are not limited to, mutations, insertions, deletions, and substitutions of one or more nucleotides. The gene may constitute an uninterrupted coding sequence or it may include one or more introns, bound by the appropriate splice junctions. The Term “gene” as used herein includes variants of the genes identified in Table 1.

The term “gene expression” refers to the process by which a nucleic acid sequence undergoes successful transcription and translation such that detectable levels of the nucleotide sequence are expressed.

The terms “gene expression profile” or “gene signature” refer to a group of genes expressed by a particular cell or tissue type wherein presence of the genes taken together or the differential expression of such genes, is indicative/predictive of a certain condition.

The term “nucleic acid” as used herein, refers to a molecule comprised of one or more nucleotides, i.e., ribonucleotides, deoxyribonucleotides, or both. The term includes monomers and polymers of ribonucleotides and deoxyribonucleotides, with the ribonucleotides and/or deoxyribonucleotides being bound together, in the case of the polymers, via 5′ to 3′ linkages. The ribonucleotide and deoxyribonucleotide polymers may be single or double-stranded. However, linkages may include any of the linkages known in the art including, for example, nucleic acids comprising 5′ to 3′ linkages. The nucleotides may be naturally occurring or may be synthetically produced analogs that are capable of forming base-pair relationships with naturally occurring base pairs. Examples of non-naturally occurring bases that are capable of forming base-pairing relationships include, but are not limited to, aza and deaza pyrimidine analogs, aza and deaza purine analogs, and other heterocyclic base analogs, wherein one or more of the carbon and nitrogen atoms of the pyrimidine rings have been substituted by heteroatoms, e.g., oxygen, sulfur, selenium, phosphorus, and the like. Furthermore, the term “nucleic acid sequences” contemplates the complementary sequence and specifically includes any nucleic acid sequence that is substantially homologous to the both the nucleic acid sequence and its complement.

The terms “array” and “microarray” refer to the type of genes or proteins represented on an array by oligonucleotides or protein-capture agents, and where the type of genes or proteins represented on the array is dependent on the intended purpose of the array (e.g., to monitor expression of human genes or proteins). The oligonucleotides or protein-capture agents on a given array may correspond to the same type, category, or group of genes or proteins. Genes or proteins may be considered to be of the same type if they share some common characteristics such as species of origin (e.g., human, mouse, rat); disease state (e.g., cancer); functions (e.g., protein kinases, tumor suppressors); or same biological process (e.g., apoptosis, signal transduction, cell cycle regulation, proliferation, differentiation). For example, one array type may be a “cancer array” in which each of the array oligonucleotides or protein-capture agents correspond to a gene or protein associated with a cancer. An “epithelial array” may be an array of oligonucleotides or protein-capture agents corresponding to unique epithelial genes or proteins. Similarly, a “cell cycle array” may be an array type in which the oligonucleotides or protein-capture agents correspond to unique genes or proteins associated with the cell cycle.

The term “cell type” refers to a cell from a given source (e.g., a tissue, organ) or a cell in a given state of differentiation, or a cell associated with a given pathology or genetic makeup.

The term “activation” as used herein refers to any alteration of a signaling pathway or biological response including, for example, increases above basal levels, restoration to basal levels from an inhibited state, and stimulation of the pathway above basal levels.

The term “differential expression” refers to both quantitative as well as qualitative differences in the temporal and tissue expression patterns of a gene or a protein in diseased tissues or cells versus normal adjacent tissue. For example, a differentially expressed gene may have its expression activated or completely inactivated in normal versus disease conditions, or may be up-regulated (over-expressed) or down-regulated (under-expressed) in a disease condition versus a normal condition. Such a qualitatively regulated gene may exhibit an expression pattern within a given tissue or cell type that is detectable in either control or disease conditions, but is not detectable in both. Stated another way, a gene or protein is differentially expressed when expression of the gene or protein occurs at a higher or lower level in the diseased tissues or cells of a patient relative to the level of its expression in the normal (disease-free) tissues or cells of the patient and/or control tissues or cells.

The term “detectable” refers to an RNA expression pattern which is detectable via the standard techniques of polymerase chain reaction (PCR), reverse transcriptase-(RT) PCR, differential display, and Northern analyses, which are well known to those of skill in the art. Similarly, protein expression patterns may be “detected” via standard techniques such as Western blots.

The term “complementary” refers to the topological compatibility or matching together of the interacting surfaces of a probe molecule and its target. The target and its probe can be described as complementary, and furthermore, the contact surface characteristics are complementary to each other. Hybridization or base pairing between nucleotides or nucleic acids, such as, for example, between the two strands of a double-stranded DNA molecule or between an oligonucleotide probe and a target are complementary.

The term “biological sample” refers to a sample obtained from an organism (e.g., a human patient) or from components (e.g., cells) of an organism. The sample may be of any biological tissue or fluid. The sample may be a “clinical sample” which is a sample derived from a patient. Such samples include, but are not limited to, sputum, blood, blood cells (e.g., white cells), amniotic fluid, plasma, semen, bone marrow, and tissue or fine needle biopsy samples, urine, peritoneal fluid, and pleural fluid, or cells therefrom. Biological samples may also include sections of tissues such as frozen sections taken for histological purposes. A biological sample may also be referred to as a “patient sample.”

A “protein” means a polymer of amino acid residues linked together by peptide bonds. The term, as used herein, refers to proteins, polypeptides, and peptides of any size, structure, or function. Typically, however, a protein will be at least six amino acids long. If the protein is a short peptide, it will be at least about 10 amino acid residues long. A protein may be naturally occurring, recombinant, or synthetic, or any combination of these. A protein may also comprise a fragment of a naturally occurring protein or peptide. A protein may be a single molecule or may be a multi-molecular complex. The term protein may also apply to amino acid polymers in which one or more amino acid residues is an artificial chemical analogue of a corresponding naturally occurring amino acid.

A “fragment of a protein,” as used herein, refers to a protein that is a portion of another protein. For example, fragments of proteins may comprise polypeptides obtained by digesting full-length protein isolated from cultured cells. In one embodiment, a protein fragment comprises at least about six amino acids. In another embodiment, the fragment comprises at least about ten amino acids. In yet another embodiment, the protein fragment comprises at least about sixteen amino acids.

As used herein, an “expression product” is a biomolecule, such as a protein, which is produced when a gene in an organism is expressed. An expression product may comprise post-translational modifications.

The term “protein expression” refers to the process by which a nucleic acid sequence undergoes successful transcription and translation such that detectable levels of the amino acid sequence or protein are expressed.

The terms “protein expression profile” or “protein expression signature” refer to a group of proteins expressed by a particular cell or tissue type (e.g., neuron, coronary artery endothelium, or disease tissue), wherein presence of the proteins taken together or the differential expression of such proteins, is indicative/predictive of a certain condition.

The term “antibody” means an immunoglobulin, whether natural or partially or wholly synthetically produced. All derivatives thereof that maintain specific binding ability are also included in the term. The term also covers any protein having a binding domain that is homologous or largely homologous to an immunoglobulin binding domain. An antibody may be monoclonal or polyclonal. The antibody may be a member of any immunoglobulin class, including any of the human classes: IgG, IgM, IgA, IgD, and IgE.

The term “antibody fragment” refers to any derivative of an antibody that is less than full-length. In one aspect, the antibody fragment retains at least a significant portion of the full-length antibody's specific binding ability, specifically, as a binding partner. Examples of antibody fragments include, but are not limited to, Fab, Fab', F(ab′)₂, scFv, Fv, dsFv diabody, and Fd fragments. The antibody fragment may be produced by any means. For example, the antibody fragment may be enzymatic ally or chemically produced by fragmentation of an intact antibody or it may be recombinantly produced from a gene encoding the partial antibody sequence. Alternatively, the antibody fragment may be wholly or partially synthetically produced. The antibody fragment may comprise a single chain antibody fragment. In another embodiment, the fragment may comprise multiple chains that are linked together, for example, by disulfide linkages. The fragment may also comprise a multimolecular complex. A functional antibody fragment may typically comprise at least about 50 amino acids and more typically will comprise at least about 200 amino acids.

Determination of Gene Expression Profiles

The following method was used to identify and validate gene expression profiles indicative of whether the patient will respond to treatment with an EGFR-TK inhibitor. Other methods for identifying gene and/or protein expression profiles are known; any of these alternative methods also could be used. See, e.g., Chen et al., NEJM, 356(1):11-20 (2007); Lu et al., PLOS Med., 3(12):e467 (2006); Golub et al., Science, 286:531-537 (1999).

The present method utilizes parallel testing in which, in one track, those genes which are over-/under-expressed as compared to normal (non-cancerous) tissue samples are identified, and, in a second track, those genes comprising chromosomal insertions or deletions as compared to normal samples are identified, from the same samples. These two tracks of analysis produce two sets of data. The data are analyzed using an algorithm which identifies the genes of the gene expression profile (i.e., those genes that are differentially expressed in cancer tissue). Positive and negative controls may be employed to normalize the results, including eliminating those genes and proteins that also are differentially expressed in normal tissues from the same patients, and confirming that the gene expression profile is unique to the cancer of interest.

In the present instance, as an initial step, biological samples from about two hundred fifty (250) patients afflicted with NSCLC were acquired. Approximately five-hundred (500) tissue samples obtained from NSCLC cancer patients were used, including tumor tissue and adjacent normal (undiseased) lung tissue. The tissue samples were obtained from patients suffering from various stages of NSCLC cancer. The samples included tumor tissue from patients who had been treated with erlotinib or gefitinib; some of the patients were responders to these compounds and others were non-responders. Clinical information associated with each sample, including treatment with erlotinib or gefitinib and the outcome of the treatment (e.g., length of survival), was recorded in a database. Clinical information also includes information such as age, sex, medical history, treatment history, symptoms, family history, recurrence (yes/no), etc. Control samples, including samples of normal (non-cancerous) lung tissue from the same patients, and other types of cancerous tissue from other patients (e.g., from a tissue repository) also were acquired. Samples of normal undiseased lung tissue from a set of healthy individuals were used as positive controls, and tumor samples from NSCLC patients who were non-responders to with erlotinib or gefitinib therapy were used as negative controls.

Gene expression profiles (GEPs) then were generated from the biological samples based on total RNA according to well-established methods. Briefly, a typical method involves isolating total RNA from the biological sample, amplifying the RNA, synthesizing cDNA, labeling the cDNA with a detectable label, hybridizing the cDNA with a genomic array, such as the Affymetrix U133 GeneChip, and determining binding of the labeled cDNA with the genomic array by measuring the intensity of the signal from the detectable label bound to the array. See, e.g., the methods described in Lu, et al., Chen, et al. and Golub, et al., supra, and the references cited therein, which are incorporated herein by reference. The resulting expression data are input into a database.

MRNAs in the tissue samples can be analyzed using commercially available or customized probes or oligonucleotide arrays, such as cDNA or oligonucleotide arrays. The use of these arrays allows for the measurement of steady-state mRNA levels of thousands of genes simultaneously, thereby presenting a powerful tool for identifying effects such as the onset, arrest or modulation of uncontrolled cell proliferation. Hybridization and/or binding of the probes on the arrays to the nucleic acids of interest from the cells can be determined by detecting and/or measuring the location and intensity of the signal received from the labeled probe or used to detect a DNA/RNA sequence from the sample that hybridizes to a nucleic acid sequence at a known location on the microarray. The intensity of the signal is proportional to the quantity of cDNA or mRNA present in the sample tissue. Numerous arrays and techniques are available and useful. Methods for determining gene and/or protein expression in sample tissues are described, for example, in U.S. Pat. No. 6,271,002; U.S. Pat. No. 6,218,122; U.S. Pat. No. 6,218,114; and U.S. Pat. No. 6,004,755; and in Wang et al., J. Clin. Oncol., 22(9):1564-1671 (2004); Golub et al, (supra); and Schena et al., Science, 270:467-470 (1995); all of which are incorporated herein by reference.

The gene analysis aspect utilized in the present method investigates gene expression as well as insertion/deletion data. As a first step, RNA was isolated from the tissue samples and labeled. Parallel processes were run on the sample to develop two sets of data: (1) over-/under-expression of genes based on mRNA levels; and (2) chromosomal insertion/deletion data. These two sets of data were then correlated by means of an algorithm. Over-/under-expression of the genes in each cancer tissue sample were compared to gene expression in the normal (non-cancerous) samples, and a subset of genes that were differentially expressed in the cancer tissue was identified. Preferably, levels of up- and down-regulation are distinguished based on fold changes of the intensity measurements of hybridized microarray probes. A difference of about 2.0 fold or greater is preferred for making such distinctions, or a p-value of less than about 0.05. That is, before a gene is said to be differentially expressed in diseased versus normal cells, the diseased cell is found to yield at least about 2 times greater or less intensity of expression than the normal cells. Generally, the greater the fold difference (or the lower the p-value), the more preferred is the gene for use as a diagnostic or prognostic tool. Genes selected for the gene signatures of the present invention have expression levels that result in the generation of a signal that is distinguishable from those of the normal or non-modulated genes by an amount that exceeds background using clinical laboratory instrumentation.

Statistical values can be used to confidently distinguish modulated from non-modulated genes and noise. Statistical tests can identify the genes most significantly differentially expressed between diverse groups of samples. The Student's t-test is an example of a robust statistical test that can be used to find significant differences between two groups. The lower the p-value, the more compelling the evidence that the gene is showing a difference between the different groups. Nevertheless, since microarrays allow measurement of more than one gene at a time, tens of thousands of statistical tests may be asked at one time. Because of this, it is unlikely to observe small p-values just by chance, and adjustments using a Sidak correction or similar step as well as a randomization/permutation experiment can be made. A p-value less than about 0.05 by the t-test is evidence that the expression level of the gene is significantly different. More compelling evidence is a p-value less then about 0.05 after the Sidak correction is factored in. For a large number of samples in each group, a p-value less than about 0.05 after the randomization/permutation test is the most compelling evidence of a significant difference.

Another parameter that can be used to select genes that generate a signal that is greater than that of the non-modulated gene or noise is the measurement of absolute signal difference. Preferably, the signal generated by the differentially expressed genes differs by at least about 20% from those of the normal or non-modulated gene (on an absolute basis). It is even more preferred that such genes produce expression patterns that are at least about 30% different than those of normal or non-modulated genes.

This differential expression analysis can be performed using commercially available arrays, for example, Affymetrix U133 GeneChip® arrays (Affymetrix, Inc., www.affymetrix.com). These arrays have probe sets for the whole human genome immobilized on the chip, and can be used to determine up- and down-regulation of genes in test samples. Other substrates having affixed thereon human genomic DNA or probes capable of detecting expression products, such as those available from Affymetrix, Agilent Technologies, Inc. (www.agilent.com) or Illumina, Inc. (www.illumina.com), also may be used. Currently preferred gene microarrays for use in the present invention include Affymetrix U133 GeneChip® arrays and Agilent Technologies genomic cDNA microarrays. Instruments and reagents for performing gene expression analysis are commercially available. See, e.g., Affymetrix GeneChip® System (www.affymetrix.com). The expression data obtained from the analysis then is input into the database.

In the second arm of the present method, chromosomal insertion/deletion data for the genes of each sample as compared to samples of normal tissue was obtained. The insertion/deletion analysis was generated using an array-based comparative genomic hybridization (“CGH”). Array CGH measures copy-number variations at multiple loci simultaneously, providing an important tool for studying cancer and developmental disorders and for developing diagnostic and therapeutic targets. Microchips for performing array CGH are commercially available, e.g., from Agilent Technologies. The Agilent chip is a chromosomal array which shows the location of genes on the chromosomes and provides additional data for the gene signature. The insertion/deletion data from this testing is input into the database.

The analyses are carried out on the same samples from the same patients to generate parallel data. The same chips and sample preparation are used to reduce variability.

The expression of certain genes known as “reference genes” “control genes” or “housekeeping genes” also is determined, preferably at the same time, as a means of ensuring the veracity of the expression profile. Reference genes are genes that are consistently expressed in many tissue types, including cancerous and normal tissues, and thus are useful to normalize gene expression profiles. See, e.g., Silvia et al., BMC Cancer, 6:200 (2006); Lee et al., Genome Research, 12(2):292-297 (2002); Zhang et al., BMC Mol. Biol., 6:4 (2005). Determining the expression of reference genes in parallel with the genes in the unique gene expression profile provides further assurance that the techniques used for determination of the gene expression profile are working properly. Any reference genes can be used in the present method and assay, including, for example, ACTB, GAPD, GUSB, RPLP0 and/or TRFC.

Data Correlation

The differential expression data and the insertion/deletion data in the database are correlated with the clinical outcomes information associated with each tissue sample also in the database by means of an algorithm to determine a gene expression profile for determining therapeutic efficacy of irinotecan, as well as late recurrence of disease and/or disease-related death associated with irinotecan therapy. Various algorithms are available which are useful for correlating the data and identifying the predictive gene signatures. For example, algorithms such as those identified in Xu et al., A Smooth Response Surface Algorithm For Constructing A Gene Regulatory Network, Physiol. Genomics 11:11-20 (2002), the entirety of which is incorporated herein by reference, may be used for the practice of the embodiments disclosed herein.

Another method for identifying gene expression profiles is through the use of optimization algorithms such as the mean variance algorithm widely used in establishing stock portfolios. One such method is described in detail in the patent application US Patent Application Publication No. 2003/0194734. Essentially, the method calls for the establishment of a set of inputs expression as measured by intensity) that will optimize the return (signal that is generated) one receives for using it while minimizing the variability of the return. The algorithm described in Irizarry et al., Nucleic Acids Res., 31:e15 (2003) also may be used. The currently preferred algorithm is the JMP Genomics algorithm available from JMP Software (www.jmp.com).

The process of selecting gene expression profiles also may include the application of heuristic rules. Such rules are formulated based on biology and an understanding of the technology used to produce clinical results, and are applied to output from the optimization method. For example, the mean variance method of gene signature identification can be applied to microarray data for a number of genes differentially expressed in subjects with cancer. Output from the method would be an optimized set of genes that could include some genes that are expressed in peripheral blood as well as in diseased tissue. If samples used in the testing method are obtained from peripheral blood and certain genes differentially expressed in instances of cancer could also be differentially expressed in peripheral blood, then a heuristic rule can be applied in which a portfolio is selected from the efficient frontier excluding those that are differentially expressed in peripheral blood. Of course, the rule can be applied prior to the formation of the efficient frontier by, for example, applying the rule during data pre-selection.

Other heuristic rules can be applied that are not necessarily related to the biology in question. For example, one can apply a rule that only a certain percentage of the portfolio can be represented by a particular gene or group of genes. Commercially available software such as the Wagner software readily accommodates these types of heuristics (Wagner Associates Mean-Variance Optimization Application, www.wagner.com). This can be useful, for example, when factors other than accuracy and precision have an impact on the desirability of including one or more genes.

As an example, the algorithm may be used for comparing gene expression profiles for various genes (or portfolios) to ascribe prognoses. The gene expression profiles of each of the genes comprising the portfolio are fixed in a medium such as a computer readable medium. This can take a number of forms. For example, a table can be established into which the range of signals (e.g., intensity measurements) indicative of disease is input. Actual patient data can then be compared to the values in the table to determine whether the patient samples are normal or diseased. In a more sophisticated embodiment, patterns of the expression signals (e.g., fluorescent intensity) are recorded digitally or graphically. The gene expression patterns from the gene portfolios used in conjunction with patient samples are then compared to the expression patterns. Pattern comparison software can then be used to determine whether the patient samples have a pattern indicative of recurrence of the disease. Of course, these comparisons can also be used to determine whether the patient is not likely to experience disease recurrence. The expression profiles of the samples are then compared to the profile of a control cell. If the sample expression patterns are consistent with the expression pattern for recurrence of cancer then (in the absence of countervailing medical considerations) the patient is treated as one would treat a relapse patient. If the sample expression patterns are consistent with the expression pattern from the normal/control cell then the patient is diagnosed negative for the cancer.

A method for analyzing the gene signatures of a patient to determine prognosis of cancer is through the use of a Cox hazard analysis program. The analysis may be conducted using S-Plus software (commercially available from Insightful Corporation, www.insightful.com). Using such methods, a gene expression profile is compared to that of a profile that confidently represents relapse (i.e., expression levels for the combination of genes in the profile is indicative of relapse). The Cox hazard model with the established threshold is used to compare the similarity of the two profiles (known relapse versus patient) and then determines whether the patient profile exceeds the threshold. If it does, then the patient is classified as one who will relapse and is accorded treatment such as adjuvant therapy. If the patient profile does not exceed the threshold then they are classified as a non-relapsing patient. Other analytical tools can also be used to answer the same question such as, linear discriminate analysis, logistic regression and neural network approaches. See, e.g., software available from JMP statistical software (www.jmp.com).

Numerous other well-known methods of pattern recognition are available. The following references provide some examples:

Weighted Voting: Golub, T R., Slonim, D K., Tamaya, P., Huard, C., Gaasenbeek, M., Mesirov, J P., Coller, H., Loh, L., Downing, J R., Caligiuri, M A., Bloomfield, C D., Lander, E S. Molecular classification of cancer: class discovery and class prediction by gene expression monitoring. Science 286:531-537, 1999.

Support Vector Machines: Su, A I., Welsh, J B., Sapinoso, L M., Kern, S G., Dimitrov, P., Lapp, H., Schultz, P G., Powell, S M., Moskaluk, C A., Frierson, H F. Jr., Hampton, G M. Molecular classification of human carcinomas by use of gene expression signatures. Cancer Research 61:7388-93, 2001. Ramaswamy, S., Tamayo, P., Rifkin, R., Mukherjee, S., Yeang, C H., Angelo, M., Ladd, C., Reich, M., Latulippe, E., Mesirov, J P., Poggio, T., Gerald, W., Loda, M., Lander, E S., Gould, T R. Multiclass cancer diagnosis using tumor gene expression signatures Proceedings of the National Academy of Sciences of the USA 98:15149-15154, 2001.

K-nearest Neighbors: Ramaswamy, S., Tamayo, P., Rifkin, R., Mukherjee, S., Yeang, C H., Angelo, M., Ladd, C., Reich, M., Latulippe, E., Mesirov, J P., Poggio, T., Gerald, W., Loda, M., Lander, E S., Gould, T R. Multiclass cancer diagnosis using tumor gene expression signatures Proceedings of the National Academy of Sciences of the USA 98:15149-15154, 2001.

Correlation Coefficients: van't Veer L J, Dai H, van de Vijver M J, He Y D, Hart A, Mao M, Peterse H L, van der Kooy K, Marton M J, Witteveen A T, Schreiber G J, Kerkhoven R M, Roberts C, Linsley P S, Bernards R, Friend S H. Gene expression profiling predicts clinical outcome of breast cancer, Nature. 2002 Jan. 31; 415(6871):530-6.

The gene expression analysis identifies a gene expression profile (GEP) unique to the cancer samples, that is, those genes which are differentially expressed by the cancer cells. This GEP then is validated, for example, using real-time quantitative polymerase chain reaction (RT-qPCR), which may be carried out using commercially available instruments and reagents, such as those available from Applied Biosystems (www.appliedbiosystems.com).

In the present instance, the results of the gene expression analysis showed that in NSCLC cancer patients who were responsive to treatment with an EGFR-TK inhibitor, the genes encoding p70S6K, phospho-S6, phospho-AKT, phospho-mTOR, phospho-pTEN, EGFR, phospho-ER, phospho-AR, AIK, osteopontin, MMP11 and GFAP are up-regulated (over-expressed) and the genes encoding phospho-p70S6, phospho MEK, phospho MAPK, phospho-IGFR/InR, phospho-EGFR and phospho-HER2/ErbB2 are down-regulated (under expressed) in patients who are responders to EGFR-TK inhibitors, compared with expression of these genes in the normal lung tissue samples from these patients, and from the negative control patients, i.e., the tissue samples from patients that had experienced a recurrence of their cancer after treatment with an EGFR-TK inhibitor. The reference genes used in the present invention, ACTB, GAPD, GUSB, RPLP0 and TRFC, all were up-regulated.

Determination of Protein Expression Profiles

Not all genes expressed by a cell are translated into proteins, therefore, once a GEP has been identified, it is desirable to ascertain whether proteins corresponding to some or all of the differentially expressed genes in the GEP also are differentially expressed by the same cells or tissue. Therefore, protein expression profiles (PEPs) are generated from the same cancer and control tissues used to identify the GEPs. PEPs also are used to validate the GEP in other colon cancer patients.

The preferred method for generating PEPs according to the present invention is by immunohistochemistry (IHC) analysis. In this method antibodies specific for the proteins in the PEP are used to interrogate tissue samples from cancer patients. Other methods for identifying PEPs are known, e.g. in situ hybridization (ISH) using protein-specific nucleic acid probes. See, e.g., Hofer et al., Clin. Can. Res., 11(16):5722 (2005); Volm et al., Clin. Exp. Metas., 19(5):385 (2002). Any of these alternative methods also could be used.

In the present instance, samples of tumor tissue and normal tissue were obtained from patients afflicted with NSCLC who had undergone successful treatment with gefitinib or with 5-FU, docetaxal or cisplatin, these are the same samples used for identifying the GEP. The tissue samples were arrayed on tissue microarrays (TMAs) to enable simultaneous analysis. TMAs consist of substrates, such as glass slides, on which up to about 1000 separate tissue samples are assembled in array fashion to allow simultaneous histological analysis. The tissue samples may comprise tissue obtained from preserved biopsy samples, e.g., paraffin-embedded or frozen tissues. Techniques for making tissue microarrays are well-known in the art. See, e.g., Simon et al., BioTechniques, 36(1):98-105 (2004); Kallioniemi et al, WO 99/44062; Kononen et al., Nat. Med., 4:844-847 (1998). In the present instance, a hollow needle was used to remove tissue cores as small as 0.6 mm in diameter from regions of interest in paraffin embedded tissues. The “regions of interest” are those that have been identified by a pathologist as containing the desired diseased or normal tissue. These tissue cores then were inserted in a recipient paraffin block in a precisely spaced array pattern. Sections from this block were cut using a microtome, mounted on a microscope slide and then analyzed by standard histological analysis. Each microarray block can be cut into approximately 100 to approximately 500 sections, which can be subjected to independent tests.

The TMAs were prepared using two tissue samples from each patient: one of NSCLC tumor tissue and one of normal lung tissue. Control arrays also were prepared; in a currently preferred embodiment, the following control TMAs were used: an array containing normal lung tissue samples from healthy, cancer-free individuals; an array of “positive controls” containing tumor tissues from cancer patients afflicted with cancers other than NSCLC, e.g., breast cancer, colon cancer, and prostate cancer; and an array of “negative controls” containing tumor samples from NSCLC cancer patients that had experienced recurrences of the cancer after treatment with an EGFR-TK inhibitor—that is, patients who were “non-responders” to the therapy.

Proteins in the tissue samples may be analyzed by interrogating the TMAs using protein-specific agents, such as antibodies or nucleic acid probes, such as aptamers. Antibodies are preferred for this purpose due to their specificity and availability. The antibodies may be monoclonal or polyclonal antibodies, antibody fragments, and/or various types of synthetic antibodies, including chimeric antibodies, or fragments thereof. Antibodies are commercially available from a number of sources (e.g., Abcam (www.abcam.com), Cell Signaling Technology (www.cellsignal.com), Santa Cruz Biotechnology (www.santacruz.com)), or may be generated using techniques well-known to those skilled in the art. The antibodies typically are equipped with detectable labels, such as enzymes, chromogens or quantum dots, which permit the antibodies to be detected. The antibodies may be conjugated or tagged directly with a detectable label, or indirectly with one member of a binding pair, of which the other member contains a detectable label. Detection systems for use with are described, for example, in the website of Ventana Medical Systems, Inc. (www.ventanamed.com). Quantum dots are particularly useful as detectable labels. The use of quantum dots is described, for example, in the following references: Jaiswal et al., Nat. Biotechnol., 21:47-51 (2003); Chan et al., Curr. Opin. Biotechnol., 13:40-46 (2002); Chan et al., Science, 281:435-446 (1998).

The use of antibodies to identify proteins of interest in the cells of a tissue, referred to as immunohistochemistry (IHC), is well established. See, e.g., Simon et al., Bio Techniques, 36(1):98 (2004); Haedicke et al., BioTechniques, 35(1):164 (2003), which are hereby incorporated by reference. The IHC assay can be automated using commercially available instruments, such as the Benchmark instruments available from Ventana Medical Systems, Inc. (www.ventanamed.com).

In the present instance, the TMAs were contacted with antibodies specific for the proteins encoded by the genes identified in the gene expression study as being up- or down-regulated in NSCLC cancer patients who were responders to therapy with an EGFR-Tk inhibitor in order to determine expression of these proteins in each type of tissue. The results of the immunohistochemical assay showed the following:

In NSCLC patients that were responsive to treatment with an EGFR-TK inhibitor, the following proteins were up-regulated: p70S6K, phospho-S6, phospho-AKT, phospho-mTOR, phospho-pTEN, EGFR, phospho-ER, phospho-AR. AIK, osteopontin, MMP11 and GFAP; and the following proteins were down-regulated: phospho-p70S6, phospho-MEK, phospho-MAPK, phospho-IGFR1/InR, phospho-EGFR and phospho-HER2, compared with an expression of these proteins in normal lung tissue from these patients and the normal lung tissue from other patients;

A majority of the EGFR-TK Inhibitor Responder Proteins were not up- or down-regulated in the positive control tissue samples; and

The EGFR-TK Inhibitor Responder Proteins were not up- or down-regulated in the negative control tissue, i.e., in the tissue samples from NSCLC patients that had experienced a recurrence of their cancer after treatment with an EGFR-TK inhibitor, specifically gefitinib (IRESSA®).

These results demonstrate that the present protein expression profiles are indicative of therapeutic efficacy of erlotinib or gefitinib in those NSCLC patients having tumors consistent with the expression profile.

Using the techniques described above, protein and gene expression profiles were generated from NSCLC patient samples, and expression profiles unique to patients responsive to therapy with erlotinib or gefitinib were identified. Fifteen proteins identified as being associated with therapeutic efficacy of these compounds are listed in Table 1 above.

Assays

The present invention further comprises methods and assays for determining whether an NSCLC patient is likely to respond to treatment with an EGFR-TK inhibitor, including erlotinib or gefitinib. According to one aspect, a formatted IHC assay can be used for determining if a tumor of an NSCLC patient cancer tumor exhibits the present GPEP. The assays may be formulated into kits that include all or some of the materials needed to conduct the analysis, including reagents (antibodies, detectable labels, etc.) and instructions.

The assay method of the invention comprises contacting a tumor sample from an NSCLC patient with a group of antibodies specific for some or all of the genes or proteins in the present GPEP, and determining the occurrence of up- or down-regulation of these genes or proteins in the samples. The use of TMAs allows numerous samples, including control samples, to be assayed simultaneously.

In a preferred embodiment, the method comprises contacting a tumor sample from an NSCLC patient with a group of antibodies specific for some or all of the proteins in the present GPEP, and determining the occurrence of up- or down-regulation of these proteins. Up-regulation of one or more of the following proteins: p70S6K, phospho-S6, phospho-AKT, phospho-mTOR, phospho-pTEN, EGFR, phospho-ER, phospho-AR, AIK, osteopontin, MMP11 and GFAP; and down-regulation of one or more of the following proteins: phospho-p70S6, phospho-MEK, phospho-MAPK, phospho-IGFR1/InR, phospho-EGFR and phospho-HER2, is indicative of the patient's responsiveness to an EGFR-TK inhibitor, such as erlotinib or gefitinib. Preferably, at least four, preferably between four and nine, and most preferably between nine and eighteen antibodies are used in the present method.

The method preferably also includes detecting and/or quantitating control or “reference proteins”. Detecting and/or quantitating the reference proteins in the samples normalizes the results and thus provides further assurance that the assay is working properly. In a currently preferred embodiment, antibodies specific for one or more of the following reference proteins are included: ACTB, GAPD, GUSB, RPLP0 and/or TRFC.

The present invention further comprises a kit containing reagents for conducting an IHC analysis of tissue samples or cells from NSCLC cancer patients, including antibodies specific for at least about four of the proteins in the GPEP and for any reference proteins. The antibodies are preferably tagged with means for detecting the binding of the antibodies to the proteins of interest, e.g., detectable labels. Preferred detectable labels include fluorescent compounds or quantum dots, however other types of detectable labels may be used. Detectable labels for antibodies are commercially available, e.g. from Ventana Medical Systems, Inc. (www.ventanamed.com).

Immunohistochemical methods for detecting protein expression in tissue samples are well known. Any method that permits the determination of expression of several different proteins can be used. See e.g., Signoretti et al., “Her-2-neu Expression and Progression Toward Androgen Independence in Human Prostate Cancer,” J. Natl. Cancer Instil., 92(23):1918-25 (2000); Gu et al., “Prostate stem cell antigen (PSCA) expression increases with high gleason score, advanced stage and bone metastasis in prostate cancer,” Oncogene, 19:1288-96 (2000). Such methods can be efficiently carried out using automated instruments designed for immunohistochemical (IHC) analysis. Instruments for rapidly performing such assays are commercially available, e.g., from Ventana Molecular Discovery Systems (www.ventanadiscovery.com) or Lab Vision Corporation (www.labvision.com). Methods according to the present invention using such instruments are carried out according to the manufacturer's instructions.

Protein specific antibodies for use in such methods or assays are readily available or can be prepared using well-established techniques. Antibodies specific for the proteins in the present GPEP can be obtained, for example, from Cell Signaling Technology, Inc. (www.cellsignal.com) or Santa Cruz Biotechnology, Inc. (www.santacruzbiotechnology.com). A comprehensive catalog of commercially available antibodies is available at www.abcam.com.

The present invention is illustrated further by the following non-limiting Example.

Example Clinical Studies

A multicenter clinical trial in the United States evaluated the tumor response rate of gefitinib (IRESSA®) at dosages of 250 and 500 mg/day in patients with advanced non-small cell lung cancer (NSCLC) whose disease had progressed after at least two prior chemotherapy regimens including a platinum drug and docetaxel. IRESSA® was taken once daily at approximately the same time each day.

Two hundred and sixteen patients received IRESSA®; 102 (47%) received a 250 mg dose and 114 (53%) received a 500 mg daily dose. Study patient demographics and disease characteristics are summarized in Table A.

TABLE A Scope of study Patient Sample Numbers Treatment 102 Patients (47%) 250 mg Iressa 114 Patients (53%) 500 mg Iressa 142 Patients Platinum and docetaxel therapies 142 Patients Positive disease progression

Forty-one percent of the patients had received two prior treatment regimens, 33% had received three prior treatment regimens, and 25% had received four or more prior treatment regimens. Effectiveness of IRESSA® as third line therapy was determined in the 142 evaluable patients with documented disease progression on platinum and docetaxel therapies or who had had unacceptable toxicity on these agents.

Tissue MicroArrays

Tissue samples obtained from the NSCLC patients in the clinical study were obtained and used to prepare tissue micro arrays (TMAs); other TMAs were prepared as controls. The TMAs used in this study are described in Table B:

TABLE B Tissue Micro Arrays Normal Screening Array This array contained samples of normal (non- cancerous) lung tissue from 200 patients (2 samples per patient) Lung Treatment EGFR This array contained 500 patient samples obtained from the NSCLC patients who had been treated with IRESSA ®): 250 tumor samples and 250 normal lung tissue samples from the same patients. Cancer screening survey Positive control array. This array contained 200 array tumor samples for cancers other than lung cancer: 50 breast cancer, 50 colon cancer, 50 prostate cancer and 50 lung cancer. Lung Progression Negative control array. This array contained samples from the NSCLC patients who progressed to the next stage of lung cancer or experience a recurrence of NSCLC after treatment with gefitinib (IRESSA ®).

The TMAs were constructed according to the following procedure:

Tissue cores from donor block containing the patient tissue samples were inserted into a recipient paraffin block. These tissue cores are punched with a thin walled, sharpened borer. An X—Y precision guide allowed the orderly placement of these tissue samples in an array format.

Presentation: TMA sections were cut at 4 microns and are mounted on positively charged glass microslides. Individual elements were 0.6 mm in diameter, spaced 0.2 mm apart.

Elements: In addition to TMAs containing the NSCLC samples, screening arrays were produced made up of pancreatic cancers, lymphoma, head and neck cancer, breast cancers and colon cancers tissue samples, 2 each from a different patient. Additional normal tissue samples were included for quality control purposes.

Specificity: The TMAs were designed for use with the specialty staining and immunohistochemical methods described below for gene expression screening purposes, by using monoclonal and polyclonal antibodies over a wide range of characterized tissue types.

Accompanying each array was an array locator map and spreadsheet containing patient diagnostic, histologic and demographic data for each element.

Immunohistochemical Staining

Immunohistochemical staining techniques were used for the visualization of tissue (cell) proteins present in the tissue samples. These techniques were based on the immunoreactivity of antibodies and the chemical properties of enzymes or enzyme complexes, which react with colorless substrate-chromogens to produce a colored end product. Initial immunoenzymatic stains utilized the direct method, which conjugated directly to an antibody with known antigenic specificity (primary antibody).

A modified labeled avidin-biotin technique was employed in which a biotinylated secondary antibody formed a complex with peroxidase-conjugated streptavidin molecules. Endogenous peroxidase activity was quenched by the addition of 3% hydrogen peroxide. The specimens then were incubated with the primary antibodies followed by sequential incubations with the biotinylated secondary link antibody (containing anti-rabbit or anti-mouse immunoglobulins) and peroxidase labeled streptavidin. The primary antibody, secondary antibody, and avidin enzyme complex is then visualized utilizing a substrate-chromogen that produces a brown pigment at the antigen site that is visible by light microscopy. Table C lists the antibodies used in this example.

TABLE C Antibody CST # Phospho-p70S6 CST #9206 Total p70S6 Kinase CST #9202 Phospho-S6 CST #2211 Phospho-AKT CST #3787 Phospho-mTOR CST #2971 Phospho-pTEN CST #9554 Phospho MEK CST #9121 Phospho MAPK CST #9106 Phospho-IGFR/InR CST #3021 Total EGFR CST #2232 Phospho-EGFR CST #2234 Phospho-HER2(ErbB2) CST #2241 Phospho-AR SC #26406-R AIK CST #4718 Phospho-ER CST #2511 CST refers to Cell Signaling Technology, Inc. SC refers to Santa Cruz Biotechnology, Inc.

Automated Immunohistochemistry Staining Procedure (IHC):

1. Heat-induced epitope retrieval (HIER) using 10 mM Citrate buffer solution, pH 6.0, was performed as follows:

-   -   a. Deparaffinized and rehydrated sections were placed in a slide         staining rack.     -   b. The rack was placed in a microwaveable pressure cooker; 750         ml of 10 mM Citrate buffer pH 6.0 was added to cover the slides.     -   c. The covered pressure cooker was placed in the microwave on         high power for 15 minutes.     -   d. The pressure cooker was removed from the microwave and cooled         until the pressure indicator dropped and the cover could be         safely removed.     -   e. The slides were allowed to cool to room temperature, and         immunohistochemical staining was carried out.         2. Slides were treated with 3% H₂O₂ for 10 min. at RT to quench         endogenous peroxidase activity.         3. Slides were rinsed gently with phosphate buffered saline         (PBS).         4. The primary antibodies were applied at the predetermined         dilution (according to Cell Signaling Technology's         Specifications) for 30 min at room temperature. Normal mouse or         rabbit serum 1:750 dilution was applied to negative control         slides.         5. Slides were rinsed with phosphate buffered saline (PBS).         6. Secondary biotinylated link antibodies* were applied for 30         min at room temperature.         7. Slides were rinsed with phosphate buffered saline (PBS).         8. The slides were treated with streptavidin-HRP (streptavidin         conjugated to horseradish peroxidase)** for 30 min at room         temperature.         9. Slides were rinsed with phosphate buffered saline (PBS).         10. The slides were treated with substrate/chromogen*** for 10         min at room temperature.         11. Slides were raised with distilled water.         12. Counterstain in Hematoxylin was applied for 1 min.         13. Slides were washed in running water for 2 min.         14. The slides were then dehydrated, cleared and the coverglass         was mounted     -   Secondary antibody: biotinylated anti-chicken and anti-mouse         immunoglobulins in phosphate buffered saline (PBS), containing         carrier protein and 15 mM sodium azide.     -   Streptavidin-HRP in PBS containing carrier protein and         anti-microbial agents from Ventana,     -   Substrate-Chromogen is substrate-imidazole-HCl buffer pH 7.5         containing H₂O₂ and anti-microbial agents,         DAB-3,3′-diaminobenzidine in chromogen solution from Ventana.

Experiment Notes:

All primary antibodies were titrated to dilutions according to manufacturer's specifications. Staining of TE30 Test Array slides (described below) was performed with and without epitope retrieval (HIER). The slides were screened by a pathologist to determine the optimal working dilution. Pretreatment with HIER provided strong specific staining with little to no background. The above immunohistochemical staining was carried out using a Benchmark instrument from Ventana Medical Systems, Inc.

Scoring Criteria:

Staining was scored on a 0-3+ scale, with 0=no staining, and trace (tr) being less than 1+ but greater than 0. The scoring procedures are described in Signoretti et al., J. Nat. Cancer Inst., Vol. 92, No. 23, p. 1918 (December 2000) and Gu et al., Oncogene, 19, 1288-1296 (2000). Grades of 1+ to 3+ represent increased intensity of staining with 3+ being strong, dark brown staining. Scoring criteria was also based on total percentage of staining 0=0%, 1=less than 25%, 2=25-50% and 3=greater than 50%. The percent positivity and the intensity of staining for both Nuclear and Cytoplasmic as well as sub-cellular components were analyzed. Both the intensity and percentage positive scores were multiplied to produce one number 0-9. 3+ staining was determined from known expression of the antigen from the positive controls either Breast Adenocarcinoma and/or LNCAP cells.

Positive, Negative and Isotype Matched Controls and Reproducibility:

Positive tissue controls were defined via western blot analysis using the antibodies listed in Table C. This experiment was performed to confirm the level of protein expression in each given control. Negative controls were also defined by the same. The positive controls consisted of Breast, Prostate, Colon and Lung cancer samples.

Positive expression was also confirmed using a Xenograft array. To make this array, SCID mice were injected with tumor cells derived from NSCLC tumors of patients shown to be responsive to gefitinib (IRESSA®), and tumors were allowed to grow. The mice then were injected with 200 mg/kg of IRESSA®, and the mice were monitored to observe responsiveness to the drug.

As a result of treatment with IRESSA®, the tumors formed in the SCID mice were reduced or eliminated. The tumors were found to have the same gene expression profile as that identified in human patients who were responders to gefitinib therapy.

Reproducibility:

All runs were grouped by antibody and tissue arrays which ensured that the runs were normalized, meaning that all of the tissue arrays were stained under the same conditions with the same antibody on the same run. A test array containing thirty negative control samples (TE 30) comprising non-cancerous tissues derived from different (non-lung) organs also was provided. This TE 30 was compared to the previous antibody run and scored accordingly. The reproducibility was compared and validated.

RESULTS

In tumor samples obtained from those NSCLC patients that were responsive to treatment with an EGFR-TK inhibitor, gefitinib, the following proteins were up-regulated: p70S6K, phospho-S6, phospho-AKT, phospho-mTOR, phospho-pTEN, EGFR, phospho-ER, phospho-AR and AIK; and the following proteins were down-regulated: phospho-p70S6, phospho-MEK, phospho-MAPK, phospho-IGFR1/InR, phospho-EGFR and phospho-HER2, compared with an expression of these proteins in normal lung tissue from these patients and the normal lung tissue from other patients. In contrast, most of these proteins were not up- or down-regulated in the positive control tissue samples. These proteins also were not up- or down-regulated in the negative control tissue, i.e., in the tissue samples from NSCLC patients that had experienced a recurrence of their cancer after treatment with gefitinib. NSCLC patients with tumors exhibiting the present gene and/or protein expression profiles had survived for a longer period of time after treatment with gefitinib compared with NSCLC patients whose tumors did not exhibit the present gene and/or protein expression profiles.

These results show that the present protein expression profile is indicative of therapeutic efficacy of erlotinib or gefitinib in those NSCLC patients having tumors consistent with the expression profile. These data support a potential role for this signature as a determinant of EGFR activity in NSCLC tumor cells and expression as a novel biomarkers for predicting clinical activity of the EGFR inhibitors erlotinib and gefitinib in NSCLC patients. 

1-3. (canceled)
 4. A method of determining if a patient diagnosed with lung cancer is a responder to treatment with an EGFR-TK inhibitor comprising: a. obtaining lung cancer tissue from the patient diagnosed with lung cancer; b. determining the level of expression in the tissue or cells of the following proteins: p70S6K comprising the amino acid sequence of SEQ ID NO. 17, phospho-S6 comprising the amino acid sequence of SEQ ID NO. 18, phospho-AKT comprising the amino acid sequence of SEQ ID NO. 19, phospho-mTOR comprising the amino acid sequence of SEQ ID NO. 20, phospho-pTEN comprising the amino acid sequence of SEQ ID NO. 21, phospho-MEK comprising the amino acid sequence of SEQ ID NO. 22, phospho-MAPK comprising the amino acid sequence of SEQ ID NO. 23, phospho-IGFR/InR comprising the amino acid sequence of SEQ ID NO. 24, EGFR comprising the amino acid sequence of SEQ ID NO. 25, phospho-HER2(ErbB2) comprising the amino acid sequence of SEQ ID NO. 26, phospho-ER comprising the amino acid sequence of SEQ ID NO. 27, phospho-AR comprising the amino acid sequence of SEQ ID NO. 28, AIK comprising the amino acid sequence of SEQ ID NO. 29, osteopontin comprising the amino acid sequence of SEQ ID NO. 30, MMP11 comprising the amino acid sequence of SEQ ID NO. 31 and GFAP comprising the amino acid sequence of SEQ ID NO. 32; and c. determining that the patient is a responder to treatment with an EGFR-TK inhibitor if the level of level of the p70S6K, phospho-S6, phospho-AKT, phospho-mTOR, phospho-pTEN, EGFR, phospho-ER, phospho-AR, AIK, osteopontin, MMP11 and GFAP is elevated in the tissue or cells as compared to the corresponding levels in normal lung tissue or cells, and the level of the phospho MEK, phospho MAPK, phospho-IGFR/InR, and phospho-HER2(ErbB2) is lower in the tissue or cells as compared to the corresponding levels in normal lung tissue or cells. 5-6. (canceled)
 7. The method of claim 4 further comprising determining the level of expression of at least one reference protein in said lung cancer tissue or cells and in said normal lung tissue or cells.
 8. The method of claim 4 wherein step (b) is performed using immunohistochemistry.
 9. The method of claim 7 wherein the reference protein is selected from the group consisting of: ACTB, GAPD, GUSB, RPLP0 and TRFC.
 10. The method of claim 1, wherein the EGFR-TK inhibitor is selected from the group consisting of gefitinib or erlotinib.
 11. The method of claim 1 wherein the type of lung cancer is non-small cell lung cancer (NSCLC). 